'''Base calling''' is the process of assigning nucleobases to chromatogram peaks, light intensity signals, or electrical current changes resulting from nucleotides passing through a nanopore. One computer program for accomplishing this job is Phred, which was a widely used base calling software program by both academic and commercial DNA sequencing laboratories because of its high base calling accuracy.<ref>{{cite journal | last=Richterich | first=Peter | title=Estimation of Errors in "Raw" DNA Sequences: A Validation Study | journal=Genome Research | publisher=Cold Spring Harbor Laboratory | volume=8 | issue=3 | date=1998-03-01 | issn=1088-9051 | pmid=9521928 | pmc=310698 | doi=10.1101/gr.8.3.251 | pages=251–259}}</ref>
Currently basecalling is commonly handled by on-instrument software, such as the proprietary Real-Time Analysis (RTA) pipeline, which is highly integrated and updated with each platform release.<ref>{{cite web |last= |first= |date= |title=Real Time Analysis (RTA) on NextSeq 1000/2000 Overview |url=https://knowledge.illumina.com/instrumentation/nextseq-1000-2000/instrumentation-nextseq-1000-2000-reference_material-list/000002441 |website= |location= |publisher=illumina |access-date=2025-08-17}}</ref>
Base callers for Nanopore sequencing like Guppy or Dorado, use neural networks trained on current signals obtained from accurate sequencing data. <ref name=wick>{{cite journal | last1=Wick | first1=Ryan R. | last2=Judd | first2=Louise M. | last3=Holt | first3=Kathryn E. | title=Performance of neural network basecalling tools for Oxford Nanopore sequencing | journal=Genome Biology | publisher=Springer Science and Business Media LLC | volume=20 | issue=1 | date=2019-06-24 | page=129 | issn=1474-760X | doi=10.1186/s13059-019-1727-y| pmid=31234903 | pmc=6591954 | doi-access=free }}</ref>
== Base calling accuracy == Base calling can be assessed by two metrics, read accuracy and consensus accuracy. Read accuracy refers to the called base's accuracy to a known reference. Consensus accuracy refers to how accurate a consensus sequence is compared to overlapping reads from the same genetic locus. <ref name=wick/>
== References == {{reflist}}
Category:Molecular biology Category:Bioinformatics